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Install and configure Conda and Bioconda
Create a .condarc in your home directory and add:
channels:
- conda-forge
- bioconda
- defaults
ssl_verify: true
conda create -n cwltool
conda install -n cwltool cwltool nodejs
conda activate cwltool
Then, all the required programs and tools will be available in the user $PATH
Using Conda as runtime environment the cwltool should be executed with the following examples:
cwltool --no-container --beta-conda-dependencies --beta-dependencies-directory /path-to-directory/storing-conda-envs
Execute cwltool with these options if Docker is installed and user has permissions to pull images:
cwltool --no-read-only --beta-use-biocontainers
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